Hello CASToR team,
I’m encountering an issue when converting GATE simulation ROOT files to CDH format for a pixelated camera. After running the conversion, the output CDH file appears empty. My key question is: Does CASToR support reconstruction of pixelated cameras at all? Could you please advise?
Hi Sharareh,
CASToR converter does support the conversion of SPECT system with pixelated cameras from ROOT data, providing the GATE macro uses the /gate/systems/SPECThead/pixel/attach line.
Could you share details about the system, the .geom file which was created/used, or any error you encountered during the conversion ?
Best,
Thibaut M.
Dear Thibaut,
I’m encountering an issue when converting GATE simulation data to CASToR format for a pixelated SPECT system. Here are the details:
System Configuration (GATE Macro Highlights)
text
Steps & Results
Request
Could you help troubleshoot:
Attached: Full [SPECT.mac] & [.geom file] for reference.
Thank you!
Sharareh
Full [SPECT.mac]:
/gate/geometry/setMaterialDatabase data/GateMaterials.db
/gate/world/geometry/setXLength 100 cm
/gate/world/geometry/setYLength 100 cm
/gate/world/geometry/setZLength 100 cm
/gate/world/daughters/name SPECThead
/gate/world/daughters/insert box
/gate/SPECThead/geometry/setXLength 8. cm
/gate/SPECThead/geometry/setYLength 9.1 cm
/gate/SPECThead/geometry/setZLength 40.1 cm
/gate/SPECThead/placement/setTranslation 7.9 0. 0.0 cm
/gate/SPECThead/setMaterial Air
/gate/SPECThead/repeaters/insert ring
/gate/SPECThead/ring/setRepeatNumber 2
/gate/SPECThead/moves/insert orbiting
/gate/SPECThead/orbiting/setSpeed 5.625 deg/s
/gate/SPECThead/orbiting/setPoint1 0 0 0 cm
/gate/SPECThead/orbiting/setPoint2 0 0 1 cm
/gate/SPECThead/vis/forceWireframe
/gate/SPECThead/daughters/name shielding
/gate/SPECThead/daughters/insert box
/gate/shielding/geometry/setXLength 5. cm
/gate/shielding/geometry/setYLength 9.1 cm
/gate/shielding/geometry/setZLength 40.1 cm
/gate/shielding/placement/setTranslation -1.5 0. 0. cm
/gate/shielding/setMaterial Lead
/gate/shielding/vis/setColor red
/gate/shielding/vis/forceWireframe
/gate/SPECThead/daughters/name collimator
/gate/SPECThead/daughters/insert box
/gate/collimator/geometry/setXLength 5. cm
/gate/collimator/geometry/setYLength 9.1 cm
/gate/collimator/geometry/setZLength 40.1 cm
/gate/collimator/placement/setTranslation -1.5 0. 0. cm
/gate/collimator/setMaterial Lead
/gate/collimator/vis/setColor red
/gate/collimator/vis/forceWireframe
/gate/collimator/daughters/name hole
/gate/collimator/daughters/insert box
/gate/hole/geometry/setXLength 5. cm
/gate/hole/geometry/setYLength 0.9 cm
/gate/hole/geometry/setZLength 0.9 cm
/gate/hole/placement/setTranslation 0. 0. 0. cm
/gate/hole/setMaterial Air
/gate/hole/repeaters/insert cubicArray
/gate/hole/cubicArray/setRepeatNumberX 1
/gate/hole/cubicArray/setRepeatNumberY 9
/gate/hole/cubicArray/setRepeatNumberZ 40
/gate/hole/cubicArray/setRepeatVector 0.0 1.0111 1.0025 cm
/gate/SPECThead/daughters/name crystal
/gate/SPECThead/daughters/insert box
/gate/crystal/geometry/setXLength 3. cm
/gate/crystal/geometry/setYLength 9.1 cm
/gate/crystal/geometry/setZLength 40.1 cm
/gate/crystal/placement/setTranslation 2.5 0. 0. cm
/gate/crystal/setMaterial Lead
/gate/crystal/daughters/name pixel
/gate/crystal/daughters/insert box
/gate/pixel/geometry/setXLength 3. cm
/gate/pixel/geometry/setYLength 0.9 cm
/gate/pixel/geometry/setZLength 0.9 cm
/gate/pixel/placement/setTranslation 0 0. 0. cm
/gate/pixel/setMaterial BGO
/gate/pixel/vis/setColor yellow
/gate/pixel/vis/forceSolid
/gate/pixel/repeaters/insert cubicArray
/gate/pixel/cubicArray/setRepeatNumberX 1
/gate/pixel/cubicArray/setRepeatNumberY 9
/gate/pixel/cubicArray/setRepeatNumberZ 40
/gate/pixel/cubicArray/setRepeatVector 0.0 1.0111 1.0025 cm
/gate/world/daughters/name Phantom
/gate/world/daughters/insert cylinder
/gate/Phantom/geometry/setRmax 1.9 cm
/gate/Phantom/geometry/setRmin 0. cm
/gate/Phantom/geometry/setHeight 29 cm
/gate/Phantom/placement/setTranslation 0. 0. 0. cm
/gate/Phantom/setMaterial PMMA
/gate/Phantom/vis/setColor blue
/gate/Phantom/vis/forceSolid
/gate/systems/SPECThead/crystal/attach crystal
/gate/systems/SPECThead/describe
/gate/Phantom/attachPhantomSD
/gate/shielding/attachPhantomSD
/gate/SPECThead/attachPhantomSD
/gate/collimator/attachPhantomSD
/gate/crystal/attachCrystalSD
/gate/pixel/attachCrystalSD
/gate/systems/SPECThead/pixel/attach pixel
/gate/physics/addProcess PhotoElectric
/gate/physics/processes/PhotoElectric/setModel StandardModel
/gate/physics/addProcess Compton
/gate/physics/processes/Compton/setModel PenelopeModel
/gate/physics/addProcess RayleighScattering
/gate/physics/processes/RayleighScattering/setModel PenelopeModel
/gate/physics/addProcess ElectronIonisation
/gate/physics/processes/ElectronIonisation/setModel StandardModel e-
/gate/physics/addProcess Bremsstrahlung
/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
/gate/physics/addProcess MultipleScattering e-
/gate/physics/processList Enabled
/gate/physics/processList Initialized
/gate/physics/Gamma/SetCutInRegion SPECThead 0.1 cm
/gate/physics/Electron/SetCutInRegion SPECThead 1.0 cm
/gate/run/initialize
/gate/source/addSource SourceConfinement
/gate/source/SourceConfinement/gps/type Volume
/gate/source/SourceConfinement/gps/shape Cylinder
/gate/source/SourceConfinement/gps/radius 1.5 cm
/gate/source/SourceConfinement/gps/halfz 14 cm
/gate/source/SourceConfinement/gps/centre 0. 0. 0. cm
/gate/source/SourceConfinement/gps/particle gamma
/gate/source/SourceConfinement/gps/energy 5 MeV
/gate/source/SourceConfinement/setActivity 30000. Bq
/gate/source/SourceConfinement/gps/angtype iso
/gate/digitizer/Singles/insert adder
/gate/digitizer/Singles/insert blurring
/gate/digitizer/Singles/blurring/setResolution 0.10
/gate/digitizer/Singles/blurring/setEnergyOfReference 5 MeV
/gate/digitizer/Singles/insert spblurring
/gate/digitizer/Singles/spblurring/setSpresolution 2.0 mm
/gate/digitizer/Singles/spblurring/verbose 0
/gate/digitizer/Singles/insert thresholder
/gate/digitizer/Singles/thresholder/setThreshold 4 MeV
/gate/digitizer/Singles/insert upholder
/gate/digitizer/Singles/upholder/setUphold 6 MeV
#/gate/digitizer/Singles/insert opticaladder
/gate/digitizer/Singles/insert readout
/gate/digitizer/Singles/readout/setDepth 2
/gate/digitizer/Singles/readout/setDepth 1
/gate/output/root/enable
/gate/output/root/setFileName benchSPECT
/gate/output/root/setRootSinglesAdderFlag 1
/gate/output/root/setRootSinglesBlurringFlag 1
/gate/output/root/setRootSinglesSpblurringFlag 1
/gate/output/root/setRootSinglesThresholderFlag 1
/gate/output/root/setRootSinglesUpholderFlag 1
/gate/output/root//setRootHitFlag 1
/gate/output/root/setRootSinglesFlag 1
/gate/output/root/setRootNtupleFlag 1
#/gate/output/ascii/setOutFileSinglesAdderFlag 0
#/gate/output/ascii/setOutFileSinglesSpblurringFlag 0
#/gate/output/ascii/setOutFileSinglesBlurringFlag 0
#/gate/output/ascii/setOutFileSinglesThresholderFlag 0
#/gate/output/ascii/setOutFileSinglesUpholderFlag 0
/gate/random/setEngineName Ranlux64
#/gate/random/setEngineSeed default
#/gate/random/setEngineSeed auto
/gate/random/setEngineSeed 123456789
#/gate/random/resetEngineFrom fileName
/gate/random/verbose 1
/gate/output/projection/enable
/gate/output/projection/setFileName YourProjection
/gate/output/projection/pixelSizeX 1 mm
/gate/output/projection/pixelSizeY 1 mm
/gate/output/projection/pixelNumberX 38
/gate/output/projection/pixelNumberY 290
/gate/output/projection/projectionPlane YZ
/gate/application/setTimeSlice 1 s
/gate/application/setTimeStart 0. s
/gate/application/setTimeStop 32. s
/gate/application/startDAQ
Full [.geom]:
modality : SPECT_CONVERGENT
scanner name : h
number of detector heads : 2
trans number of pixels : 9
trans pixel size : 9
trans gap size : 1.111
axial number of pixels : 40
axial pixel size : 9
axial gap size : 1.025
detector depth : 30
scanner radius : 79,79
head1:
trans focal model: constant
trans number of coef model: 1
trans parameters: 0
axial focal model: constant
axial number of coef model: 1
axial parameters: 0
head2:
trans focal model: constant
trans number of coef model: 1
trans parameters: 0
axial focal model: constant
axial number of coef model: 1
axial parameters: 0
voxels number transaxial : 20
voxels number axial : 101
field of view transaxial : 39.5
field of view axial : 401
description : SPECT camera extracted from GATE macro: /home/gate/cam11/SPECT.mac
Hi Sharareh,
The geometry file appears to be consistent with your simulation indeed.
I don’t see any potential issue for the conversion in your mac file, but if you get an empty Cdh file and no Cdf file, something must have gone wrong during the conversion of the root data.
Did you get any error message ? What output do you get if you increase verbosity (add -vb 2 to castor-GATERootToCastor command line) ?
Best,
Thibaut
Hi,
Possibly a ROOT related issue judging from the error. Could you double check root global variables were correctly initialized?
If everything seems fine, maybe you could share me a link to the root file so that I could try to reproduce the error on my end and check what is wrong.
Best,
Hi
Root file share link: https://drive.google.com/file/d/1wj9xyZAHyA4ocOdkqnENRL1YSy5DSsxW/view?usp=sharing
Thank you very much
Hi Sharareh,
The problem seems to come from some latest updates of the code, which broke the conversion for SPECT pixelated cameras. Could you retry with the following version and let me know if the issue remains ?
Best,
Thibaut
Hi
Thank you for your help. The SPECT pixelated camera conversion issue is fixed with the latest code update. 
Quick question:
Can the FBP algorithmbe used for reconstruction in CASToR?
Best regards,
Hello,
No there is no implementation of FBP with CASToR. The datafile format makes it difficult to implement a reconstruction like FBP which assumes that the data are organized as true sinograms/projections.
Best,
Thank you very much🙏
